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parallel: Better error message if Text::CSV is not installed.
This commit is contained in:
Ole Tange
parent
77e9f59abb
commit
e40d44c517
25
NEWS
25
NEWS
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@ -8,21 +8,30 @@ New in this release:
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News about GNU Parallel:
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* Distributed Task Processing with GNU Parallel https://www.youtube.com/watch?v=usbMLggdMgc
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* Distributed Task Processing with GNU Parallel
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https://www.youtube.com/watch?v=usbMLggdMgc
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* GNU Parallel workflow for many small, independent runs https://docs.csc.fi/support/tutorials/many/
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* GNU Parallel workflow for many small, independent runs
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https://docs.csc.fi/support/tutorials/many/
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* Copy a File To Multiple Directories With A Single Command on Linux https://www.linuxfordevices.com/tutorials/linux/copy-file-to-multiple-directories-with-one-command
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* Copy a File To Multiple Directories With A Single Command on Linux
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https://www.linuxfordevices.com/tutorials/linux/copy-file-to-multiple-directories-with-one-command
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* Behind The Scenes: The Power Of Simple Command Line Tools At Cloud Scale https://blog.gdeltproject.org/behind-the-scenes-the-power-of-simple-command-line-tools-at-cloud-scale/
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* Behind The Scenes: The Power Of Simple Command Line Tools At Cloud
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Scale
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https://blog.gdeltproject.org/behind-the-scenes-the-power-of-simple-command-line-tools-at-cloud-scale/
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* Run lz4 compression in parallel using GNU parallel https://www.openguru.com/2022/09/
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* Run lz4 compression in parallel using GNU parallel
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https://www.openguru.com/2022/09/
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* Xargs / Parallel With Code Examples https://www.folkstalk.com/2022/09/xargs-parallel-with-code-examples.html
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* Xargs / Parallel With Code Examples
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https://www.folkstalk.com/2022/09/xargs-parallel-with-code-examples.html
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* Parallel processing on a single node with GNU Parallel https://www3.cs.stonybrook.edu/~cse416/Section01/Slides/SeaWulfIntro_CSE416_09222022.pdf
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* Parallel processing on a single node with GNU Parallel
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https://www3.cs.stonybrook.edu/~cse416/Section01/Slides/SeaWulfIntro_CSE416_09222022.pdf
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* Using GNU parallel painlessly -- from basics to bioinformatics job orchestration https://www.youtube.com/watch?v=qypUdm-IE9c
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* Using GNU parallel painlessly -- from basics to bioinformatics job
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orchestration https://www.youtube.com/watch?v=qypUdm-IE9c
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20220922
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@ -4,6 +4,9 @@
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Quote of the month:
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[GNU Parallel] is the most amazing tool ever invented for bioinformatics!
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-- Istvan Albert https://www.ialbert.me/
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Got around to using GNU parallel for the first time from a suggestion by @jdwasmuth ... now I'm wishing I started using this years ago
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-- Stefan Gavriliuc @GavriliucStefan@twitter
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51
src/parallel
51
src/parallel
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@ -2278,7 +2278,11 @@ sub parse_options(@) {
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if(defined $opt::tmuxpane) { $opt::tmux = $opt::tmuxpane; }
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if(defined $opt::colsep) { $Global::trim = 'lr'; }
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if(defined $opt::csv) {
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$Global::use{"Text::CSV"} ||= eval "use Text::CSV; 1;";
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if(not $Global::use{"Text::CSV"} ||= eval "use Text::CSV; 1;") {
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::error("The perl module Text::CSV is not installed.");
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::error("Try installing libtext-csv-perl or perl-Text-CSV.");
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wait_and_exit(255);
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}
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$opt::colsep = defined $opt::colsep ? $opt::colsep : ",";
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my $csv_setting = { binary => 1, sep_char => $opt::colsep };
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my $sep = $csv_setting->{sep_char};
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@ -2698,7 +2702,7 @@ sub check_invalid_option_combinations() {
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sub init_globals() {
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# Defaults:
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$Global::version = 20221022;
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$Global::version = 20221115;
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$Global::progname = 'parallel';
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$::name = "GNU Parallel";
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$Global::infinity = 2**31;
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@ -3551,18 +3555,18 @@ sub shell_quote_scalar_default($) {
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# $string = string to be quoted
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# Returns:
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# $shell_quoted = string quoted as needed by the shell
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my $s = $_[0];
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if($s =~ /[^-_.+a-z0-9\/]/i) {
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$s =~ s/'/'"'"'/g; # "-quote single quotes
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$s = "'$s'"; # '-quote entire string
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$s =~ s/^''//; # Remove unneeded '' at ends
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$s =~ s/''$//; # (faster than s/^''|''$//g)
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return $s;
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} elsif ($s eq "") {
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local $_ = $_[0];
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if(/[^-_.+a-z0-9\/]/i) {
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s/'/'"'"'/g; # "-quote '-quotes
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$_ = "'$_'"; # '-quote entire string
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s/^''//; # Remove unneeded '' at ends
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s/''$//; # (faster than s/^''|''$//g)
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return $_;
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} elsif ($_ eq "") {
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return "''";
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} else {
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# No quoting needed
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return $s;
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return $_;
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}
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}
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@ -13152,19 +13156,22 @@ sub real_max_length() {
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sub find_max($) {
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my $string = shift;
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# This is slow on Cygwin, so give Cygwin users a warning
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if($^O eq "cygwin") {
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if($^O eq "cygwin" or $^O eq "msys") {
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::warning("Finding the maximal command line length. ".
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"This may take up to 1 minute.")
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}
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# Use an upper bound of 100 MB if the shell allows for infinite
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# long lengths
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my $upper = 100_000_000;
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my $lower;
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# 1000 is supported everywhere, so the search can start anywhere 1..999
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# 324 makes the search much faster on Cygwin, so let us use that
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my $len = 324;
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do {
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if($len > $upper) { return $len };
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$lower = $len;
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$len *= 16;
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::debug("init", "Maxlen: $lower<$len<$upper(".($upper-$lower)."): ");
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} while (is_acceptable_command_line_length($len,$string));
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# Then search for the actual max length between
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# last successful length ($len/16) and upper bound
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@ -13190,7 +13197,7 @@ sub binary_find_max($$$) {
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# Guessing too high is cheap. Guessing too low is expensive.
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my $split = ($^O eq "cygwin" or $^O eq "msys") ? 0.93 : 0.5;
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my $middle = int (($upper-$lower)*$split + $lower);
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::debug("init", "Maxlen: $lower<$middle<$upper: ");
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::debug("init", "Maxlen: $lower<$middle<$upper(".($upper-$lower)."): ");
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if (is_acceptable_command_line_length($middle,$string)) {
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return binary_find_max($middle,$upper,$string);
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} else {
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@ -13198,22 +13205,6 @@ sub binary_find_max($$$) {
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}
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}
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sub _binary_find_max($$$) {
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# Given a lower and upper bound find the max (length or args) of a
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# command line
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# Returns:
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# number of chars on the longest command line allowed
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my ($lower, $upper, $string) = (@_);
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if($lower == $upper or $lower == $upper-1) { return $lower; }
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my $middle = int (($upper-$lower)/2 + $lower);
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::debug("init", "Maxlen: $lower<$middle<$upper: ");
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if (is_acceptable_command_line_length($middle,$string)) {
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return binary_find_max($middle,$upper,$string);
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} else {
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return binary_find_max($lower,$middle,$string);
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}
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}
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{
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my $prg;
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@ -13232,7 +13223,7 @@ sub _binary_find_max($$$) {
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# Force using non-built-in command
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$prg ||= ::which("echo");
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::qqx("$prg ".${string}x(($len-1-length $prg)/length $string));
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::debug("init", "$len=$? ");
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::debug("init", "$len=$?\n");
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return not $?;
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}
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}
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@ -988,15 +988,15 @@ B<env_parallel>
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Show the estimated number of seconds before finishing.
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This forces GNU B<parallel> to read all jobs before starting to find
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the number of jobs. GNU B<parallel> normally only reads the next job
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to run.
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the number of jobs (unless you use B<--total-jobs>). GNU B<parallel>
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normally only reads the next job to run.
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The estimate is based on the runtime of finished jobs, so the first
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estimate will only be shown when the first job has finished.
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Implies B<--progress>.
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See also: B<--bar> B<--progress>
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See also: B<--bar> B<--progress> B<--total-jobs>
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=item B<--fg>
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@ -1028,6 +1028,9 @@ Beware: If the fifo is never opened for reading, the job will block forever:
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seq 1000000 | parallel --fifo echo This will block
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seq 1000000 | parallel --fifo 'echo This will not block < {}'
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By using B<--fifo> instead of B<--cat> you may save I/O as B<--cat>
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will write to a temporary file, whereas B<--fifo> will not.
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Implies B<--pipe> unless B<--pipe-part> is used.
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See also: B<--cat> B<--pipe> B<--pipe-part>
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@ -1203,11 +1206,11 @@ Example:
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=item Z<> --halt now,fail=1
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exit when the first job fails. Kill running jobs.
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exit when a job has failed. Kill running jobs.
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=item Z<> --halt soon,fail=3
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exit when 3 jobs fail, but wait for running jobs to complete.
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exit when 3 jobs have failed, but wait for running jobs to complete.
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=item Z<> --halt soon,fail=3%
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@ -1215,11 +1218,11 @@ exit when 3% of the jobs have failed, but wait for running jobs to complete.
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=item Z<> --halt now,success=1
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exit when a job succeeds. Kill running jobs.
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exit when a job has succeeded. Kill running jobs.
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=item Z<> --halt soon,success=3
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exit when 3 jobs succeeds, but wait for running jobs to complete.
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exit when 3 jobs have succeeded, but wait for running jobs to complete.
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=item Z<> --halt now,success=3%
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@ -1227,11 +1230,11 @@ exit when 3% of the jobs have succeeded. Kill running jobs.
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=item Z<> --halt now,done=1
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exit when one of the jobs finishes. Kill running jobs.
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exit when a job has finished. Kill running jobs.
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=item Z<> --halt soon,done=3
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exit when 3 jobs finishes, but wait for running jobs to complete.
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exit when 3 jobs have finished, but wait for running jobs to complete.
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=item Z<> --halt now,done=3%
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@ -1340,6 +1343,8 @@ See also: B<{}>
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=item B<--joblog> I<logfile>
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=item B<--jl> I<logfile>
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Logfile for executed jobs.
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Save a list of the executed jobs to I<logfile> in the following TAB
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@ -4,6 +4,13 @@
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#
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# SPDX-License-Identifier: GPL-3.0-or-later
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par_csv_not_installed() {
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echo '### Give error if CSV.pm is not installed when using --csv'
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sudo parallel mv {} {}.hidden ::: /usr/share/perl5/Text/CSV.pm
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stdout parallel --csv echo ::: this should give an error
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sudo parallel mv {}.hidden {} ::: /usr/share/perl5/Text/CSV.pm
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}
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par_sem_dir() {
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echo '### bug #58985: sem stall if .parallel/semaphores is chmod 0'
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chmod 0 ~/.parallel/semaphores
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@ -5,6 +5,9 @@ par_bug56403 3 job3cjob3d
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par_bug56403 1 job1a
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par_bug56403 1 job1b
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par_bug56403 2 job2cjob2d
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par_csv_not_installed ### Give error if CSV.pm is not installed when using --csv
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par_csv_not_installed parallel: Error: The perl module Text::CSV is not installed.
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par_csv_not_installed parallel: Error: Try installing libtext-csv-perl or perl-Text-CSV.
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par_delay_Xauto TODO: --retries for those that fail and --sshdelay
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par_delay_Xauto ### bug #58911: --delay Xauto
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par_delay_Xauto 0
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